Alpha-1 antitrypsin deficiency (AATD) is an inherited genetic disorder that affects the level and function of alpha-1 antitrypsin (AAT). AAT is a serine protease inhibitor (PI) that is mainly produced in the liver but also in alveolar macrophages (AM) and pulmonary epithelial cells. Neutrophil elastase (NE), the primary target of AAT, degrades elastin in the pulmonary alveoli leading to parenchymal destruction and subsequent emphysema1. Instinctively, replacement therapy (augmentation therapy) with exogenous AAT to restore the level of AAT to above the protective threshold level, should solve the problem but there is controversy whether augmentation therapy is sufficiently efficacious. The goal of this study, an ancillary proposal to the Genomic Research in Alpha-1 Anti-trypsin Disease and Sarcoidosis (GRADS), is to define the changes in epigenetic alterations (histone modifications) in alveolar macrophages before and after augmentation therapy and their potential association with disease phenotype through comparison with healthy control samples. Our proposal is unique and complementary to the parent study as we are focusing on specific changes in epigenetic histone modifications in alveolar macrophages before and after augmentation therapy, whereas the parent grant will be assessing whole cell mRNA and miRNA expression. Our proposal is also time-sensitive as histone analysis requires freshly isolated cells and not stored DNA samples. We propose three aims to address our hypothesis that the environmentally influenced, variable pattern of histone modifications that can modulate AM mediated inflammation and can contribute to a variable clinical course of AATD, may also be influenced by or influence the molecular activity of AAT augmentation therapy. Using a novel approach that has not been undertaken in AATD but proven in other inflammatory pulmonary and non-pulmonary disorders, in Aim 1 we will compare the epigenomic signature of specific inflammation-associated histone post-translational modifications in AATD alveolar macrophages (AM) from PiZZ subjects before and after 6 months of AAT augmentation therapy via Chromatin Immuno-Precipitation coupled with next generation sequencing (ChIP-seq). In Aim 2 we will elucidate the AATD alveolar macrophage (AM) epigenetically regulated transcription profile via computational integration of AM RNA-seq gene expression data sets with ChIP-seq and in Aim 3, we will analyze the effects of histone modifying enzyme ex vivo treatment, such as HDACi treatment, on AATD associated AM gene expression and cell function. In all three aims, we incorporate healthy control samples to elucidate AATD- specific epigenetic and transcriptional signature. This project will elucidate the effect of augmentation therapy on the epigenetic signature of AM in AATD patients, enhancing our understanding of the immunomodulatory mechanisms regulating AATD and providing an epigenetic map for potentially targeted treatment.